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Am J Transplant. 2019 May;19(5):1278-1287. doi: 10.1111/ajt.15316. Epub 2019 Mar 20.

Single cell immune profiling in transplantation research.

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Department of Medicine/Nephrology, Stanford University, Palo Alto, California.
Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, California.
Department of Medicine/Biomedical Informatics, Stanford University, Stanford, California.
VA Palo Alto Health Care System, Palo Alto, California.


Recently developed single-cell profiling technologies hold promise to provide new insights including analysis of population heterogeneity and linkage of antigen receptors with gene expression. These technologies produce complex data sets that require knowledge of bioinformatics for appropriate analysis. In this minireview, we discuss several single-cell immune profiling technologies for gene and protein expression, including cytometry by time-of-flight, RNA sequencing, and antigen receptor sequencing, as well as key considerations for analysis that apply to each. Because of the critical importance of data analysis for high parameter single cell analysis, we discuss essential factors in analysis of these data, including quality control, quantification, examples of methods for high dimensional analysis, immune repertoire analysis, and preparation of analysis pipelines. We provide examples of, and suggestions for, application of these innovative methods to transplantation research.


basic (laboratory) research/science; flow cytometry; genetics; genomics; immunobiology; informatics; molecular biology; translational research/science


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